text: # -*- coding: utf-8 -*-
  
  # Copyright 2019 Novo Nordisk Foundation Center for Biosustainability,
  # Technical University of Denmark.
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  
  """Structurally validate SBML-formatted file input."""
  
  
  from __future__ import absolute_import
  
  from warnings import catch_warnings, simplefilter
  
  import libsbml
  from cobra.io import read_sbml_model
  
  
  def load_cobra_model(path, notifications):
      """Load a COBRA model with meta information from an SBML document."""
      doc = libsbml.readSBML(path)
      fbc = doc.getPlugin("fbc")
      sbml_ver = doc.getLevel(), doc.getVersion(), fbc if fbc is None else \
          fbc.getVersion()
      with catch_warnings(record=True) as warnings:
          simplefilter("always")
          try:
              model = read_sbml_model(path)
          except Exception as err:
              notifications['errors'].append(str(err))
              model = None
              validate = True
          else:
              validate = False
          notifications['warnings'].extend([str(w.message) for w in warnings])
      if validate:
          run_sbml_validation(doc, notifications)
      return model, sbml_ver
  
  
  def format_failure(failure):
      """Format how an error or warning should be displayed."""
      return "Line {}, Column {} - #{}: {} - Category: {}, Severity: {}".format(
          failure.getLine(),
          failure.getColumn(),
          failure.getErrorId(),
          failure.getMessage(),
          failure.getCategoryAsString(),
          failure.getSeverity()
      )
  
  
  def run_sbml_validation(document, notifications):
      """Report errors and warnings found in an SBML document."""
      validator = libsbml.SBMLValidator()
      validator.validate(document)
      for i in range(document.getNumErrors()):
          notifications['errors'].append(format_failure(document.getError(i)))
      for i in range(validator.getNumFailures()):
          failure = validator.getFailure(i)
          if failure.isWarning():
              notifications['warnings'].append(format_failure(failure))
          else:
              notifications['errors'].append(format_failure(failure))
  